It's true Muscovy's are terrible to herd. I have two border collies and an Australian Kelpie and have herded ducks at ASCA trials before. The only breeds you want to herd are Indian Runners and/or Khaki Cambells. Your ducks must have been trained using some other stimulus to go where you want them to go. I don't know of anyone that uses them for herding purposes. In my experience the majority of people who use ducks to train their herding dogs generally stick to the Indian Runners because they naturally group together when under stress, like sheep do.Muscovy can definitely be herded, i do it everyday with our flock and earlier this year i had 17 of them i put in, the ducks all taught the younger ones how to do this.
As for a chicken vs duck? eh, sounds like dogs and cats to me, both serve purpose, both have pros & cons. I keep both and will continue too. It truly falls down to what you need & want, not one being inferior to another.